Synthesis and Structural Characterization of the N2G−Mitomycin C−N2G Interstrand Cross-Link in a Model Synthetic 23 Base Pair Oligonucleotide DNA Duplex

1996 ◽  
Vol 9 (7) ◽  
pp. 1063-1071 ◽  
Author(s):  
Amy J. Warren ◽  
Joshua W. Hamilton
Keyword(s):  
Mitomycin C ◽  
Structural Characterization ◽  
Base Pair ◽  
Cross Link ◽  
Dna Duplex

scholarly journals Application of Molecular Mass Spectrometry for The Structural Characterization of a DNA-Protein Cross-Links

2018 ◽  
Vol 62 (2) ◽  
Author(s):  
Jiawei Gong ◽  
Morwena Jane Solivio ◽  
Edward J Merino ◽  
Julio Alberto Landero Figueroa
Keyword(s):  
Mass Spectrometry ◽  
Small Molecule ◽  
Structural Characterization ◽  
Peptide Sequencing ◽  
Ionization Mass ◽  
Cross Link ◽  
Ms Analysis ◽  
Cross Links ◽  
The Cross

<p>To date, many different analytical methods have been used to investigate the cross-linking reaction mechanism and to obtain the chemical structure of DNA-Protein Cross-links (DPCs). Direct MS analysis of DPCs is challenging because of the ionization properties of DNA and the protein. However, peptide sequencing and mass spectrometry (MS) as analytical techniques are playing increasingly important roles for the structure determination of DPCs model. In our previous study, a novel approach was presented for purification, detection and quantification of DPCs by newly developed inductively coupled plasma mass spectrometry (ICPMS/MS), which allows sub-ppb detection of S and P, key heteroelements in DNA and proteins.</p><p>In this study, we enhanced our previously developed method and it was complemented by the use of molecular MS to allow complete characterization of a DNA-protein cross-link.  First, a small molecule model is utilized to identify the adduct structure that will likely occur in an intact DNA-protein cross-link.  We investigate the thermal stability of DNA-protein cross-links, both in an intact DPC and a small molecule adduct to determine feasibility of digestion/thermal degradationof DNA without the cross-link information being lost.  Thermal degradation was conducted to reduce the cross-linked DNA into a single nucleoside. The remaining protein-nucleoside adduct then was proteolytically digested, generating a peptide-nucleoside adduct. The absence of the phosphate moiety allows for facile structural characterization <em>via</em> electrospray ionization mass spectrometry (ESI-MS).  Additional calculations were done for peptide matching allowing us to determine the cross-link location in the protein, made possible <em>via</em> MS/MS analysis.  Additionally, we show that steric effects play an important role in DPC formation.</p>

Structural Characterization of a DNA Duplex Modeled on a DNA:RNA Hybrid of the Polypurine Tract Recognized by a Reverse Transcriptase

1998 ◽  
Vol 17 (4) ◽  
pp. 831-841 ◽  
Author(s):  
Mayumi Kanagawa ◽  
Yutaka Okada ◽  
Sciichi Uesugi ◽  
Hirofumi Doi ◽  
Masato Katahira
Keyword(s):  
Reverse Transcriptase ◽  
Structural Characterization ◽  
Dna Duplex ◽  
Polypurine Tract

New ultrastructural findings about Borrelia burgdorferi by cryofixation, negative staining, thin sectioning and scanning techniques

1990 ◽  
Vol 48 (3) ◽  
pp. 582-583
Author(s):  
S. F. Hayes ◽  
M. D. Corwin ◽  
T. G. Schwan ◽  
D. W. Dorward ◽  
W. Burgdorfer
Keyword(s):  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Structural Characterization ◽  
Negative Staining ◽  
Low Speed ◽  
Thin Sectioning ◽  
Ultrastructural Findings

Characterization of Borrelia burgdorferi strains by means of negative staining EM has become an integral part of many studies related to the biology of the Lyme disease organism. However, relying solely upon negative staining to compare new isolates with prototype B31 or other borreliae is often unsatisfactory. To obtain more satisfactory results, we have relied upon a correlative approach encompassing a variety EM techniques, i.e., scanning for topographical features and cryotomy, negative staining and thin sectioning to provide a more complete structural characterization of B. burgdorferi.For characterization, isolates of B. burgdorferi were cultured in BSK II media from which they were removed by low speed centrifugation. The sedimented borrelia were carefully resuspended in stabilizing buffer so as to preserve their features for scanning and negative staining. Alternatively, others were prepared for conventional thin sectioning and for cryotomy using modified procedures. For thin sectioning, the fixative described by Ito, et al.

Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90

2011 ◽  
Vol 44 (06) ◽  
Author(s):  
A Bracher ◽  
C Kozany ◽  
AK Thost ◽  
F Hausch
Keyword(s):  
Structural Characterization ◽  
Ppiase Domain
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